Thursday, March 7, 2013

BAC Report- Midterm #2

funny test answers

The BAC meet yesterday at 4 PM.  During the meeting the committee reviewed all of the comments that you submitted. After discussion they met with me to discuss the following four questions.

1. Question 18 Blue and 21 Pink

It appears that the confusion about this question arose over whether the answers related to only the reactions listed in each prompt or the entire process.  The question is intended to relate only to what is occurring in each answer prompt.  So the correct answer is e) none of the above.

Some students thought that they should interpret the question by examining whether the entire process could produce ATP.  Because photosystems are involved in photosythesis then answer (a) would be correct.  Because both lactic acid fermentation and alcohol fermentation are part of anaerobic respiration both answers b and c could be correct.  However, there is no choice for "all of the above" which would be the correct answer if the question is interpreted this way.

Answer (e) remains the only correct answer.

2. Question 24 Blue and 29 Pink

I did not really understand the confusion related to this question.  Some people apparently thought that I must be talking about CAM plants in answer (a) because CAM plants close their stomata at night (no light conditions, not low light conditions).  The information in answer (a) is not accurate because plants do not close their stomata in low light conditions.

Answer (c) remains the only correct answer.

3.  Question 33 Blue and 37 Pink

I found this absorption spectrum of carotene from a study on the internet.  To answer this question correctly I expected you to know (1) that the photosynthetic pigments found in C3 plants like ferns were chlorophyll a and b and carotene.  I expected that you would all know that chlorophyll is green and that the reason it is green is that it reflects the green wavelengths of light and absorbs the other wavelengths.  Thus, green pigments have two major absorption peaks at the low end and high end of the visible light wavelengths and reflects the wavelengths in the middle.
Carotene is orange so it reflects the yellows, reds, and oranges and absorbs the rest.

In order to understand what absorption spectrums should look like you need to understand the relationship between wavelength and color (see Figure 10.6 in the book).

The confusion about this question apparently arises about whether the slight increase in absorbance that occurs around 670-680 nm is an absoprtion peak.  From reading the graph you see that this pigment asborbs less than 10% of the light of this wavelength.   Clearly, this little blip on the graph does indicate an absorption peak at longer wavelengths.  (saying that blip is an absorption peak is equivalent to defining where the overpass of the loop passes slide road, the highest point in Lubbock, as a mountain).

It is not possible for a pigment that reflects virtually all light larger than 600 nm to appear to be green.  Thus, the pigment shown in the figure must, by analysis of the absorption spectrum and by elimination be carotene.

When I met with the BAC representatives yesterday afternoon I told them that I would accept (a) Chlorophyll a as a correct answer as well.  However, after giving this much too much thought over night, I have decided that chlorophyll a is not an acceptable answer for this question.  Sorry to have changed my mind, but I think that this is the correct way to reward students with a strong understanding of how to interpret absporption spectrums.

Answer (c) remains the only correct answer.

4. Question 50 Blue and Question 3 Pink

Apparently, confusion with this question arose over the term "facts".  I tried to make it clear that there were parts of the climate change story that were "facts" that virtually every body agreed upon and other parts of the story were conclusions drawn from different kinds of evidence.

It is a fact that the atmospheric concentration of carbon dioxide has increased over the last 50 years (see the Mauna Loa curve) and that carbon dioxide functions as a green house gas.  It is also a fact that the global climate models that include the effects of human activity on atmospheric carbon dioxide concentration predict the temperature changes that have occurred over the last century than the models that excluded the effects of humans.  This led the IPCC to conclude that it was "very likely" that humans have caused global climate change.  This represents the best current conclusion drawn by the world's experts on this subject, but does not represent a fact.

Answer (d) remains the only correct answer.

The answers shown in the previous blog post are the correct answers for this exam.

Thanks again to the members of the BAC for investing the time and effort in attempting to make the testing process for BIOL 1404 as fair as possible.



Wednesday, March 6, 2013

Answer Key For Midterm #2



Here are what I currently think are the correct answers to the exam questions.  I will meet with the BAC at 4 PM this afternoon and this evening I will report on the results of that meeting.

Form 1 (Blue)

1 c
2 b
3 d
4 c
5 a
6 b
7 b- (I incorrectly listed c as the correct answer on the posted exam, that was wrong)
8  all correct (I have decided that I don't like this question, so all answers will be correct)
9 b
10 c
11 a
12 b
13 b
14 e
15 d
16 c
17 d
18 e
19 c
20 b
21 b
22 c
23 d
24 c
25 e
26 b
27 a
28 a
29 a
30 e
31 a
32 c
33 c
34 d
35 e
36 c
37 e
38 b
39 d
40 e
41 e
42 d
43 b
44 d
45 d
46 b
47 c
48 a
49 a
50 d

Form 2 (Pink)

1 a
2 a
3 d
4 c
5 b
6 d
7 c
8 a
9 b
10 all correct (I have decided that I don't like this question, so all answers will be correct)
11 e
12 b
13 c
14 a
15 b
16 b
17 e
18 d
19 c
20 d
21 e
22 c
23 b
24 b
25 c
26 b
27 e
28 d
29 c
30 e
31 a
32 a
33 a
34 e
35 a
36 c
37 c
38 d
39 c
40 e
41 b
42 d
43 e
44 e
45 d
46 b
47 d
48 d
49 b
50 c


Tuesday, March 5, 2013

Only a politician could link aerobic respiration and the global carbon cycle in this manner!



Enjoy!


State lawmaker defends bike tax, says bicycling is not good for the environment



http://www.seattlebikeblog.com/2013/03/02/state-lawmaker-says-bicycling-is-not-good-for-the-environment-should-be-taxed/

Monday, March 4, 2013

Jeffrey's SI Review Videos


If Jeffrey can't make it as an SI Instructor he can always focus on his dance moves.

Here are the links to the videos from Jeffrey's Marathon Review session for the second midterm.

Photosynthesis Part 1:
http://www.youtube.com/watch?v=UCQstcx3MGA

Photosynthesis Part 2:
http://www.youtube.com/watch?v=2KafICuWyVc

Cellular Respiration:
http://www.youtube.com/watch?v=mpy2G7_rils

Aunt Molly's World; Intro to Plants
http://www.youtube.com/watch?v=kiIyhuJOgNg

Plants Part 1:
http://www.youtube.com/watch?v=1564RLg_LTk

Plants Part 2:

http://www.youtube.com/watch?v=9yIa07lfVDQ

Plants Part 3:

http://www.youtube.com/my_videos_edit?video_id=OD-Ab7Gpplo&video_referrer=watch&ns=1&feature=mhsn

Friday, March 1, 2013

Plant Diversity- Seed Plants





Lecture Video: http://mediacast.ttu.edu/Mediasite/Play/47f1c8f46666481ab3aae2b64abbb8d31d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b


Gymosperms and angiosperms are the "seed plants".

Readings From Textbook

pages 618 - 635.

Gymnosperms

Expected Learning Outcomes


By the end of this course a fully engaged student should be able to

- defne and contrast homospory and heterospory
- discuss the evolutionary advantage of heterosporty over homospory
- identify the parts of a seed and discuss why reproducing by seeds is an advantaged compared to reproducing by spores
- discuss the life cycle of a pine
- discuss the characteristics of pines that are advanced relative to the ferns and those that are primitive relative to the angiosperms

Angiosperms

Expected Learning Outcomes


At the end of the course a fully engaged student should be able to

- discuss the parts of a flower
- discuss the evolutionary advantage of reproducing by flowers rather than by cones
- discuss the life cycle of an angiosperm
- discuss the characteristics of angiosperms that are advanced relative to the pines and those that are primitive relative to the angiosperms
- discuss why angiosperms are the most successful of all plant groups

Thursday, February 28, 2013

SI, Marathon Reviews, and Group OH for the 2nd Midterm

Here are the schedules for the remaining SI sessions, the SI Leaders' Marathon Reviews and my Group OH.

Thursday: Jeffrey: 6-7:30pm HH104

MARATHONS:
Thursday: Suzanne: 7-10pm Bio LH100
Sunday: Jeffrey 2-5pm Bio LH100

Group OH
Monday: 6:30 - ?? Bio room 21

Homework Assignment #4

HW #4 is now available on Mastering Biology.

Wednesday, February 27, 2013

Plant Diversity- Ferns



Ferns are examples of the first vascular plants.

Readings From Textbook

pages 610 - 617


Lecture Video: http://mediacast.ttu.edu/Mediasite/Play/bd420633464742c09ae19a749929d3661d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b



Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discuss the components of the vascular system
- discuss the advantage of a having a vascular system
- diagram the life cycle of a fern
- discuss the morphological and physiological characteristics of ferns
- discuss the characteristics of ferns that makes them considered to be advanced relative to mosses but primitive relative to the gumnosperms
- discuss how the morphological and life history characteristics limits their size and geographic distrubution

Tuesday, February 26, 2013

Homework Assignments 2 and 3

The second homework assignment, covering cellular respiration, is currently available on the MasteringBiology website.  The due date for this assignment is Saturday March 2nd by 11:59 PM (really, I have set the time correctly!!).

The third homework assignment, covering primitive plants, will become available on Wednesday February 27th.  The due date for this assignment is Monday March 4th by 11:59 PM.

Keep an eye out for my final homework assignment that will be due before the exam on Tuesday March 5th.

Homework #1- Update

Hello Everyone,

Thanks to everyone who sent me a message letting me know that I had set the completion time for HW #1 for 11:50 AM rather than 11:59 PM as I intended.  Because so many of you contacted me I am unable to respond to all of you individually.

The purpose of the homework problems are to encourage you to spend more time studying the material.  Because it is not fair to punish anyone for a mistake that I made, ALL STUDENTS WILL RECEIVE THE FULL 12 POINTS FOR THE FIRST HW ASSIGNMENT.


Thursday, February 21, 2013

Plant Diversity- Algae and Mosses



Plants are interesting to me because they are so different from us and the organisms that we are most familiar with (mostly animals). At first these differences will cause unfamiliarity, but eventually you will not be so bogged down by learning new vocabulary and you will hopefully come to realize that plants are more interesting than you might have thought (and besides, no plants means no dorritos, french fries, or beer?).


Lecture Videos: http://mediacast.ttu.edu/Mediasite/Play/970d298352ea462587ecf88d87bae3421d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b


http://mediacast.ttu.edu/Mediasite/Play/bd420633464742c09ae19a749929d3661d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b





Readings From Textbook

pages 600 - 610.

Further Viewing

1) Here is the slideshow that I will use in class for the final three lectures.

http://www.slideshare.net/secret/DBv71wnKTH1YBN

2) Here is a powerpoint presentation from a group called "world of teaching" that covers plant diversity? There are many "quiz questions" that should be helpful to look at.

http://www.worldofteaching.com/powerpoints/biology/Plant%20Divisions.ppt

Primitive Plants

Expected Learning Outcomes

A the end of this course a fully engaged student should be able to

- functionally define a plant
- discuss the characteristics of a primitive plant such as Chlamydomonas
- diagram a life cycle of a human
- diagram the life cycle of Chlamydomonas
- distinguish between oogamy and isogamy
- discuss the evolutionary advantage of multicellularity, diploid dominance, and oogamy

Transition to Land

Expected Learning Outcomes


By the end of this course a fully engaged student should be able to

- discuss the problems plants face when moving to the land
- discuss the characteristics of the ancestor of land plants
- diagram the life cycle of a moss
- discuss the morphological and physiological characteristics of mosses
- discuss the characteristics of mosses that makes them considered to be advanced relative to primitive plants but primitive relative to the ferns
- discuss how the morphological and life history characteristics of mosses limits their growth and geographic distribution

Tuesday, February 19, 2013

Mastering Biology: Homework Assignment #1



On-line homework will account for a portion of your grade for BIOL 1404. You will need to be enrolled in the MasteringBiology website. Below is a message from Dr. Dini explaining what you need to do in order to enroll. Students who took BIOL 1403 here last semester should be familiar with the system. Those of you who are new to BIOL 1404 at Tech might check with fellow students about the on-line homework because they are likely to know much more about it than I do.

The first assignment will be due by 11:59 PM on Monday February 25th. I have posted the first assignment that relates to Photysynthesis

Mark McG

Dear Student:
In this course you will be using MasteringBiology™, an online tutorial and homework companion to your textbook. It may be useful to print this sheet before you attempt to register.

Students who were enrolled in the on-line homework for BIOL 1403 no longer need their access code, as they are already in the system. They just have to click on the button to enroll in a new course, and it’s done. They merely need the new course’s ID #. New students DO need an access code (unless Mastering Biology was used wherever they took BIOL 1403).


What You Need:
P A valid email address
P A password that you make up (must have 8 characters; at least 1 of these must be a letter and at least one of these must be a number.) If you already have a Pearson Education account (you probably do if you took BIOL 1403 at TTU last semester of if you use MasteringPhysics or MyMathLab), just use the same password.
P A student access code (Comes in the Student Access Kit that may have been packaged with your new textbook or is available separately in your school’s bookstore. Otherwise, you can purchase access online at www.masteringbiology.com.)
P The ZIP code for Texas Tech University: 79409
P The Course ID:  MBMCGINLEY45100
P Your TTU ID#: _____________________ (Please DO include the R at the start of your number.  Memorize this #, if you have not already done so)

Register
Go to www.masteringbiology.com and click New Students under Register.
· To register using the Student Access Code inside the MasteringBiology Student Access Kit, select Yes, I have an access code. Click Continue.

–OR– Purchase access online: Select No, I need to purchase access online now. Click Continue, and then follow the on-screen instructions to purchase access using a credit card or PayPal. The purchase path includes registration, but the process may differ slightly from the steps printed here.
· License Agreement and Privacy Policy: Click I Accept to indicate that you have read and agree to the license agreement and privacy policy.
· Select the appropriate option under “Do you have a Pearson Education account?” and supply the requested information. If you are taking or have taken Math or Physics classes at TTU that used a Pearson textbook and had on-line assignments, you may already have a Pearson account. If so, you are encouraged to use the same login name and password as before. Upon completion, the Confirmation & Summary page confirms your registration. This information will also be emailed to you for your records. You can either click Log In Now or return to www.masteringbiology.com later.

Log In
Go to www.masteringbiology.com.
Enter your Login Name and Password and click Log In.

Enroll in Your Instructor’s Course and/or Access the Self-Study Area
Upon first login, you’ll be prompted to either:
Enter your instructor’s MasteringBiology Course ID and click Save; OR
Select your text and Go to Study Area

Do the first of these. Under Student ID, you will need to enter your personal TTU R# so that your scores can be recorded and downloaded to the grading spreadsheet.

Congratulations! You have completed registration and have enrolled in your instructor’s MasteringBiology course. To access your course from now on, simply go to www.masteringbiology.com, enter your Login Name and Password, and click Log In. If your instructor has created assignments, you can access them by clicking on the Assignment List button. Otherwise, click on Study Area to access self-study material.

System Requirements & Support
To effectively use the resources on this website, check its system requirements:
Log in to www.masteringbiology.com and click the “System requirements” link at the bottom of the home page. In particular, you may need to check that the latest version of the Flash player is available to your browser.
Customer Support: http://www.masteringbiology.com/support.

Dr. Dini, Dr. McGinley, or Ms. Monje do NOT supply customer service or tech support. If you experience problems with the website, contact the company. You can communicate with customer support via e-mail, chat, or telephone. Try submitting your first assignment well before the deadline because if you have trouble and need to communicate with customer support, their response time may be up to 48 h if via e-mail, or quicker via chat.

Cellular Respiration



Cellular respiration converts chemical energy in glucose to chemical energy in ATP which is the ultimate source of energy used to do "biological work".

Readings From Textbook

Pages 163 - 183
Lecture Video- http://mediacast.ttu.edu/Mediasite/Play/970d298352ea462587ecf88d87bae3421d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b

Powerpoint Presentation

http://www.slideshare.net/MarkMcGinley/cellular-respiration-11758578

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discus glycolysis, anaerobic respiration, alcohol fermentation, lactic acid fermentation, aerobic respiration, the Kreb's Cycle, and electron transport
- compare and contrast aerobic respiration with anaerobic respiration
- discus why the breakdown of glucose to produce ATP is so much more efficient when oxygen is present
- describe where in the cell the different parts of cellular respiration take place

Why Are Plants Green? or Why Aren't Plants Black



If I was hired as an engineer to design a machine whose job was to convert light energy into chemical energy I probably would not choose to use a green pigment. Instead, I would choose to use a black pigment because black pigments would absorb more energy because they would absorb all wavelengths of light. If you look at a field of plants you will notice that they are green (OK this doesn't work too well around Lubbock in the winter)and we have learned that chlorophyll, a green pigment, is the dominant photosynthetic pigment. What is going on?

Here is one theory about why chlorophyll is the dominant photosynthetic pigment in plants today. Early on there were photosynthetic bacteria with purple pigments (purple is a combination of red and violet). These aquatic bacteria had a very simple sort of cyclic electron flow that was able to convert light energy into energy in ATP (they didn't have non-cyclic flow or the Calvin Cycle).

Origin of chlorophyll- The purple pigment absorbed all wavelengths of light except for the reds and violets. Thus, any bacteria using purple pigments that lived deeper in the water than the purple bacteria on the surface would have no light to use because it had all been absorbed by the surface bacteris (exploitative competition). Because red and violet wavelengths pass through to deeper water, bacteria that contained a pigment that was able to absorb these wavelengths would be able to coexist with the purple bacteria. This was the origin of chlorophyll.

Competition purple and green photosynthetic pigments. Over time there was competition between organisms with purple photosynthetic pigments and green photosynthetic pigments. Obviously, the green photosynthetic pigments won this competition because chlorophyll is the dominant photosynthetic pigment today (there are still examples of photosynthetic bacteria with purple pigments, but they are limited to very harsh environments). Interestingly, chlorophyll came to dominate, not because it was a better at absorbing light energy, but rather because the cyclic flow machinery associated with chlorophyll was more efficient at producing ATP than the machinery associated with the purple pigment was. Thus, it is an evolutionary accident that modern plants are green.

Black Plants

It would be possible for modern plants to be black if they had enough accessory pigments to allow them to absorb all wavelengths of light. In fact, some red algae that live deep below the surface where light levels are low are basically black. Because the amount of light is not the factor that limits the rate of photosynthesis in most terrestrial plants, it is not worth the cost of producing extra accessory pigments. However, deep in the ocean where light levels are low, plants benefit from being able to absorb all wavelengths of light so deep marine algae have invested in extra accessory pigments.

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discuss why terrestrial plants to not invest in the accessory pigments required to make them black

Factors LImiting the Rate of Photosynthesis



The graph above shows how the rate of photosynthesis is affected by irradiance (light level) and the concentration of carbon dioxide.

The rate of photosynthesis can be limited by a variety of environmental factors including

1) light
2) concentration of carbon dioxide
3) water
4) soil nutrients

Which factor most limits photosynthesis varies between environments.

Light- Can directly limit the rate of photosythesis by limiting the rate at which ATP and NADPH are produced.

Carbon dioxide- can directly limit the rate of photosynthesis by limiting the rate at which the Calvin Cyle takes place.

Water- can indirectly limit the rate of photosynthesis. When plants are water stressed they close their stomata (long before the concentration of water in the cell becomes too low for water to supply electrons to P680). Thus, the rate of photosynthesis is water stressed plants is directly limited by the amount of carbon dioxide in the leaf.

Soil Nutrients- Sometimes the rate limiting step in photosynthesis is the rate at which carbon dioxide + RuBP ==> PGA. This reaction is catalyzed by the enzyme RuBP carboxylase. Increasing the amount of RuBP carboxlyase in the cell can increase the rate at which this reaction occurs. Fertilizing plants with nitrogen will increase the amount of RuBP Carboxylase produced by the plant.

Expected Learning Outcomes

By the end of this class a fully engaged student should be able to

- discuss the factors that can directly or indirectly limit the rates of photosynthesis
- discuss how the most limiting factors should vary between environments
- discuss how the activities of farmers such as irrigation and fertilization can increase photosynthetic rates
- interpret the graph at the top of the post (irradiance measures light intensity and the three lines represent different concentrations of carbon dioxide)
- explain what why the graph shows that shape

Carbon Fixation





Technically, carbon fixation is defined as the first chemical reaction that incorporates carbon dioxide into an organic molecule (a molecule with more than one carbon atom).

In C3 photosynthesis the following step is considered to be carbon fixation-

carbon dioxide + RuBP ==> PGA

In CAM photosynthesis the following is considered to be carbon fixation-

carbon dioxide ===> malate

Note: CAM plants also have the reaction- carbon dioxide + RuBP ===> PGA, but in this case this step is not considered to be carbon fixation.

Sometimes people will loosely use the term carbon fixation to mean the production of glucose by photosynthesis. Be sure that you are aware of how different authors are using the term and you should attempt to use the term as precisely as possible in your own work.

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- define carbon fixation
- identify carbon fixation in C3 and CAM photosynthesis

Monday, February 18, 2013

Stomatal Function and CAM Photosynthesis




Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- describe patterns of stomatal opening in C3 plants
- describe CAM photosynthesis
- discuss why CAM photosynthesis is an adaptation in desert enviornments
- discuss why all plants do not use CAM photosynthesis


Lecture Video: http://mediacast.ttu.edu/Mediasite/Play/c952faeba33546d3b8910e6e1bbf716c1d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b



Powerpoint Presentation

http://www.slideshare.net/MarkMcGinley/stomatal-function-and-cam-photosynthesis

Saturday, February 16, 2013

Leaf Structure



Lecture Video: http://mediacast.ttu.edu/Mediasite/Play/c952faeba33546d3b8910e6e1bbf716c1d?catalog=4dc7289a-d3e0-4ae5-8fdc-5b86c027a06b




In most plants, leaves are the major sites of photosynthesis. Thus, we can think of leaves as "photosynthesis machines" and use our knowledge of natural selection to try to understand aspects of leaf structure.

Further Reading

http://micro.magnet.fsu.edu/cells/leaftissue/leaftissue.html

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discuss important differences between animals and plants in gas uptake
- diagram the cross section of a leaf
- discuss the characteristics and purpose of the cuticle, stomata, spongy mesophyl cells, and the palisade cells.
- explain the adaptive basis of leaf structure

Some Suggestions About How to Study About Photosynthesis



Photosynthesis is a complicated and complex process.  I find that many students focus so much on learning about the details that they lose focus on the big picture.

I suggest that you first review the powerpoint presentation I showed in class and then review the relevant material in the book. Next, I would look at the Expected Learning Outcomes in the blog posts on the Light Dependent and Light Independent reactions.  Make sure that you check out the animations. They all use a slightly different approach to cover the same process. You might also try some of the end of the chapter review materials.

 I suggest that you write out answers to all of the expected learning outcomes. Most of these are relatively short. After you have done this you should be able to answer the following three questions.

1) Describe the process of photosynthesis in only one sentence.

2) Describe the process of photosynthesis in only one paragraph.

3) Explain the process of photosynthesis in full detail.

In order to perform well on the test you should be able to explain the material to a fellow classmate.
I think that you can learn a lot by critiquing the answers of your fellow classmates and suggesting how to improve their answers (I find that it is always easier to critique someone else's work than it is to critique my own). Hopefully, the feedback you receive will help you to determine whether you have mastered the material at a deep level or not.

If you would like me to review your written answers to the Expected Learning Outcomes email them to me and I will take a look and get back to you.